The overarching rationale for this project is that emerging technologies for next-generation sequencing allow the comprehensive determination of genomes, transcriptomes, and other complex populations of nucleic acid, but on their own do not permit resolution of signal from individual cells within complex populations. This is a significant limitation in multiple settings where information about intercellular heterogeneity is needed. These include the analysis of rare virus-infected cells in large populations as well as the global understanding of highly diverse and complex populations. To address this need, this project seeks to employ microfluidics to generate stable, uniform emulsions in which single cells are encapsulated at limiting dilution. Thus, tens of millions of single-cell reaction chambers can be created. Various adaptations of next-generation sequencing library preparation technology are then employed to generate material for sequencing that capture information about intercellular heterogeneity within cell populations studied.